rs6922541

Positions:

• chr6-135161681-A-C
• chr6-135161681-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.512 in 151,968 control chromosomes in the GnomAD database, including 22,148 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (22148 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77698 AN: 151850 Hom.: 22098 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.501

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.512 AC: 77810 AN: 151968 Hom.: 22148 Cov.: 31 AF XY: 0.510 AC XY: 37860 AN XY: 74232

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.504

Alfa AF: 0.431 Hom.: 7433

Bravo AF: 0.530

Asia WGS AF: 0.590 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6922541; hg19: chr6-135482819;